1de Duve Institute, UCLouvain, Brussels, Belgium
2Institute for Biomedicine, Eurac Research, Italy
3Department of Anaesthesiology and Intensive Care, University Medicine Greifswald, Germany
*order of authors defined by sample with a random seed of 42
https://github.com/jorainer/spectra_workshop

RforMassSpectrometry

  • Initiative to create a flexible and scalable infrastructure for MS data.
  • Streamline development efforts.
  • Ensure high quality code (documentation, unit tests and code review process).
  • See Laurent Gatto’s poster for details and the web page for ways to contribute.

Status quo

The plan

The plan

  • Splitting MSnbase simplifies re-use of functionality.
  • Get real infrastructure for MS data.

Mass spectrum

  • Spectrum:
    • 2 numeric: m/z and intensity values.
    • additional metadata information.
  • MSnbase: Spectrum object for a single spectrum.

Mass spectrum

… but usually we deal with many spectra …

Think bigger: Spectra

  • One object to represent data from one or many spectra.

Think flexible: MsBackend

  • Separate user functionality from data handling and storage.

Think flexible: MsBackend

  • Separate user functionality from data handling and storage.
  • Enables use of different backends (in-memory/on-disk, remote files, SQL-based, …).

The whole picture

The interactive part

Installation instructions:

install.packages("BiocManager")
BiocManager::install(c("remotes", "magrittr", "rmarkdown"))
BiocManager::install("RforMassSpectrometry/Spectra")
BiocManager::install("RforMassSpectrometry/MsBackendHmdb")
BiocManager::install(c("mzR", "BiocStyle"))

Get the data and code:

git clone https://github.com/jorainer/spectra_workshop